Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

BroadInternalArrays and BroadInternalImputation: change docker from dockerhub to gcr #828

Merged
merged 8 commits into from
Sep 30, 2022
Merged

BroadInternalArrays and BroadInternalImputation: change docker from dockerhub to gcr #828

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
2ce31b0
change from dockerhub to gcr
schaluva Sep 20, 2022
b6ee9b8
update changelogs
schaluva Sep 20, 2022
1d040da
Merge branch 'develop' into emerge_gcr_images
schaluva Sep 21, 2022
26853dc
Merge branch 'develop' into emerge_gcr_images
schaluva Sep 22, 2022
a876f97
Merge branch 'develop' into emerge_gcr_images
schaluva Sep 30, 2022
cc4f741
update arrays changelog
schaluva Sep 30, 2022
cd0eb6e
arrays changelogs updated with gcr image
schaluva Sep 30, 2022
bc3b8a3
update changelogs
schaluva Sep 30, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion pipelines/broad/arrays/imputation/Imputation.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 1.1.5
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated BCFTools/VCFTools and Minimac4 Docker images to fix vulnerabilities.
* Updated tasks FormatImputationOutputs, FormatImputationWideOutputs, and IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.1.4
2022-08-23 (Date of Last Commit)
Expand Down
3 changes: 2 additions & 1 deletion pipelines/broad/arrays/single_sample/Arrays.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 2.6.15
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
* Updated tasks FormatArraysOutputs and IngestOutputsToTDR with GCR images instead of Dockerhub.

# 2.6.14
2022-09-07 (Date of Last Commit)
Expand Down
3 changes: 2 additions & 1 deletion pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 1.16.0
2022-09-07 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated task IngestOutputsToTDR in InternalTasks.wdl with new docker tag to accommodate changes for BroadInternalArrays pipeline. Change has no effect on this pipeline.
* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.15.9
2022-06-15 (Date of Last Commit)
Expand Down
3 changes: 2 additions & 1 deletion ...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 1.0.4
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.0.3
2022-09-20 (Date of Last Commit)
Expand Down
3 changes: 2 additions & 1 deletion ..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 1.0.4
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.0.3
2022-09-20 (Date of Last Commit)
Expand Down
6 changes: 4 additions & 2 deletions pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,19 @@
# 1.1.1
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python, BCFTools/VCFTools, and Minimac4 Docker images to fix vulnerabilities.
* Updated tasks FormatImputationOutputs, FormatImputationWideOutputs, and IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.1.0
2022-09-06 (Date of Last Commit)
2022-09-20 (Date of Last Commit)

* Updated call to IngestOutputsToTDR to remove 'prefix_column'. Python script has been updated and not longer requires this input parameter.
* Update task IngestOutputsToTDR to not require 'prefix_column'. Python script has been updated and not longer requires this input parameter.

* Update task FormatImputationOutputs with new docker tag.
* Update task FormatImputationWideOutputs with new docker tag.
* Update task IngestOutputsToTDR with new docker tag.
* Update tasks FormatImputationOutputs, FormatImputationWideOutputs, and IngestOutputsToTDR with GCR image instead of DockerHub image.

# 1.0.9
2022-08-29 (Date of Last Commit)
Expand Down
7 changes: 4 additions & 3 deletions pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,18 @@
# 1.0.7
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
* Updated tasks FormatArraysOutputs and IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.0.6
2022-09-02 (Date of Last Commit)
2022-09-20 (Date of Last Commit)

* Updated call to IngestOutputsToTDR to remove 'prefix_column'. Python script has been updated and not longer requires this input parameter.
* Update task IngestOutputsToTDR to not require 'prefix_column'. Python script has been updated and not longer requires this input parameter.

* Update task FormatArraysOutputs with new docker tag.
* Update task IngestOutputsToTDR with new docker tag.

* Update tasks FormatArraysOutputs and IngestOutputsToTDR with GCR image instead of DockerHub image.

# 1.0.5
2022-08-29 (Date of Last Commit)
Expand Down
3 changes: 2 additions & 1 deletion .../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 1.0.5
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.0.4
2022-09-20 (Date of Last Commit)
Expand Down
3 changes: 2 additions & 1 deletion pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 1.0.18
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.0.17
2022-09-07 (Date of Last Commit)
Expand Down
3 changes: 2 additions & 1 deletion pipelines/broad/qc/CheckFingerprint.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# 1.0.9
2022-09-23 (Date of Last Commit)
2022-09-30 (Date of Last Commit)

* Updated Picard-Python Docker image in Utilities.wdl to fix vulnerabilities.
* Updated task IngestOutputsToTDR with GCR images instead of Dockerhub.

# 1.0.8
2022-09-07 (Date of Last Commit)
Expand Down
2 changes: 1 addition & 1 deletion tasks/broad/InternalArraysTasks.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -541,7 +541,7 @@ task FormatArraysOutputs {
>>>

runtime {
docker: "broadinstitute/horsefish:eMerge_09022022"
docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
}

output {
Expand Down
4 changes: 2 additions & 2 deletions tasks/broad/InternalImputationTasks.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ task FormatImputationOutputs {
>>>

runtime {
docker: "broadinstitute/horsefish:eMerge_09022022"
docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
}

output {
Expand Down Expand Up @@ -115,7 +115,7 @@ task FormatImputationWideOutputs{
>>>

runtime {
docker: "broadinstitute/horsefish:eMerge_09022022"
docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
}

output {
Expand Down
2 changes: 1 addition & 1 deletion tasks/broad/InternalTasks.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ task IngestOutputsToTDR {
}

runtime {
docker: "broadinstitute/horsefish:eMerge_09022022"
docker: "gcr.io/emerge-production/emerge_wdls:emerge_09022022"
}

output {
Expand Down